The Englishman entered the final day at Doha Golf Club level with his compatriot at the top of the leaderboard. He opened up a three-shot lead at the turn, but an impressive fightback by Fisher meant the pair were separated by a just single stroke as they went up the par five last.
It was advantage Fisher after two shots, with Pepperell in the rough after both men laid up. However, Pepperell hit an excellent third to set up a par which his playing partner could only match.
Pepperell's closing round of 70 got him to 18 under, with Fisher signing for a 71, one shot back, and Swede Marcus Kinhult finishing at 16 under after a 68. Spanish duo Gonzalo Fernandez-Castaño and Pablo Larrazábal, Frenchman Grégory Havret and Italian Renato Paratore shared fourth place at 15 under.
"What a day,” said Pepperell, after receiving the iconic Mother of Pearl Trophy for winning his maiden European Tour title in his 129th appearance. “Oli made it really tough and I made it tough for myself at the end there with the second shot at 18.
"I felt good all day, I felt comfortable. I didn't feel that comfortable with my swing, but I was in a great place mentally and I kept telling myself that I'm going to win this.
"Oli certainly made life more interesting. Relief is the number one emotion as is always the case with a win, although I haven't had many.
The victory was just reward for Pepperell’s mental fortitude and hard work after fighting back from losing his Tour card and returning to Q-School in 2016.
"This will give me confidence,” he said. “When you win, you know you can win. I've always felt and believed I will win out here, but it hadn't happened before today. You've always got to take that step and that's not easy, but at some point in everyone's career they've got to do something for the first time. Hopefully this is not my last.”
Pepperell won the ALLIANZ Open Côtes d'Armor Bretagne en route to graduating from the Challenge Tour in 2012 and then enjoyed three consistent seasons before losing his card, leading to a successful trip Q-School to regain it immediately.
His bounceback season was a triumph, securing four top fives and three top tens from his last ten events in 2017. A slow start to the current season saw him miss cuts in his first two outings, before signs of improvement at last week’s NBO Oman Open.
"The last nine months have been great. The start of the season's been a little bit sloppy, haven't really had my game in a good spot. I worked with somebody slightly different this week and it made a nice difference. I found it a little easier out there today to go and trust the feeling that I had.
For Fisher, it is a first top three since the 2014 Africa Open, but he will have to wait a little longer to add to his 2011 Czech Open title.
“It went all the way to the last hole which, after my front nine, was what I was hoping for on the back nine,” he said. “I hit a lot of good shots coming down the back nine and gave myself a lot of good chances, but there were just too many bogeys today – four in total – so you’re never going to win a tournament making that many mistakes on a Sunday. But at least I pressed him all the way.”
South African George Coetzee and German Sebastian Heisele finished at 14 under, a shot clear of England's Matthew Baldwin, Frenchman Mike Lorenzo-Vera and Spain's Adrian Otaegui.